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Structure paper

TitleInterrogating HIV Integrase for Compounds that Bind- a Sampl Challenge.
Journal, issue, pagesJ. Comput. Aided Mol. Des., Vol. 28, Page 347-, Year 2014
Publish dateNov 11, 2013 (structure data deposition date)
AuthorsPeat, T.S. / Dolezal, O. / Newman, J. / Mobley, D. / Deadman, J.J.
External linksJ. Comput. Aided Mol. Des. / PubMed:24532034
MethodsX-ray diffraction
Resolution1.65 - 2.15 Å
Structure data

PDB-4ce9:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-4cea:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-4ceb:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-4cec:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-4ced:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-4cee:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-4cef:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-4ceo:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-4ceq:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-4cer:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-4ces:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-4cez:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-4cf0:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-4cf1:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-4cf2:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-4cf8:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-4cf9:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-4cfa:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 2.05 Å

PDB-4cfb:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-4cfc:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-4cfd:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-4cgd:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-4cgf:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-4cgg:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-4cgh:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.76 Å

PDB-4cgi:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 2.07 Å

PDB-4cgj:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-4chn:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-4cho:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-4chp:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-4chq:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-4chy:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-4chz:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-4cie:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-4cif:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-4cig:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-4cj3:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-4cj4:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-4cj5:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-4cje:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-4cjf:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-4cjk:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-4cjl:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.77 Å

PDB-4cjp:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-4cjq:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-4cjr:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-4cjs:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-4cjt:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.71 Å

PDB-4cju:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-4cjv:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-4cjw:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-4ck1:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-4ck2:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-4ck3:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.79 Å

PDB-4ovl:
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

Chemicals

ChemComp-SO4:
SULFATE ION

ChemComp-ACY:
ACETIC ACID

ChemComp-GOL:
GLYCEROL

ChemComp-O3N:
(2S)-2-(2-carboxyethyl)-6-{[{2-[(cyclohexylmethyl)carbamoyl]benzyl}(prop-2-en-1-yl)amino]methyl}-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

ChemComp-HOH:
WATER

ChemComp-CL:
Unknown entry

ChemComp-ZSW:
(R)-[2-[[(2R)-butan-2-yl]carbamoyl]phenyl]methyl-[[(2S)-5-carboxy-2-(2-carboxyethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]methyl]-prop-2-enyl-azanium

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-ZSV:
(R)-[(2S)-5-carboxy-2-(2-carboxyethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]methyl-[[2-[(4-methoxyphenyl)methylcarbamoyl]phenyl]methyl]-prop-2-enyl-azanium

ChemComp-ACT:
ACETATE ION

ChemComp-2SS:
(2S)-6-[[[2-(cyclobutylmethylcarbamoyl)phenyl]methyl-prop-2-enyl-amino]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

ChemComp-9NS:
(2S)-6-[[[2-(furan-2-ylmethylcarbamoyl)phenyl]methyl-prop-2-enyl-amino]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

ChemComp-B0T:
(2S)-6-[[[2-[[(2S)-butan-2-yl]carbamoyl]phenyl]methyl-methyl-amino]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

ChemComp-D0T:
(2S)-2-(3-hydroxy-3-oxopropyl)-6-[[methyl-[[2-[(phenylmethyl)carbamoyl]phenyl]methyl]amino]methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

ChemComp-G0T:
(2S)-2-(3-hydroxy-3-oxopropyl)-6-[[[2-[(4-methoxyphenyl)methylcarbamoyl]phenyl]methyl-methyl-amino]methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

ChemComp-QCH:
(2S)-6-[[[2-(cyclohexylmethylcarbamoyl)phenyl]methyl-methyl-amino]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM

ChemComp-VL4:
(2S)-6-[[[2-(cyclobutylmethylcarbamoyl)phenyl]methyl-methyl-amino]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

ChemComp-NFW:
(2S)-6-[[[2-(furan-2-ylmethylcarbamoyl)phenyl]methyl-methyl-amino]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

ChemComp-O5U:
(2R)-6-[[(1R,2S)-2-(6-azanylhexanoylamino)-2,3-dihydro-1H-inden-1-yl]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

ChemComp-IY7:
(2s)-6-[[(1r,2s)-2-(5-azanylpentanoylamino)-2,3-dihydro-1h-inden-1-yl]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

ChemComp-3GM:
(2s)-6-[[(1r,2s)-2-(4-azanylbutanoylamino)-2,3-dihydro-1h-inden-1-yl]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

ChemComp-V7H:
(2S)-2-(3-hydroxy-3-oxopropyl)-6-[[[2-[(phenylmethyl)carbamoyl]phenyl]methylamino]methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

ChemComp-5EY:
(3R)-3-(3-hydroxy-3-oxopropyl)-6-[(E)-[(2R)-2-oxidanyl-2,3-dihydroinden-1-ylidene]methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

ChemComp-EE2:
(2R)-2-(3-hydroxy-3-oxopropyl)-6-[(E)-[(2S)-2-oxidanyl-2,3-dihydroinden-1-ylidene]methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

ChemComp-WOP:
5-[[methyl-[[(1S)-2-oxidanylidene-1-phenyl-2-[(phenylmethyl)amino]ethyl]carbamoyl]amino]methyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-OM3:
(R)-(4-CARBOXY-1,3-BENZODIOXOL-5-YL)METHYL-[[2-(CYCLOHEXYLMETHYLCARBAMOYL)PHENYL]METHYL]-METHYL-AZANIUM

ChemComp-7NV:
5-[[[(1S)-2-(butylamino)-2-oxidanylidene-1-phenyl-ethyl]carbamoyl-methyl-amino]methyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-S8Y:
5-[[[(1R)-2-(tert-butylamino)-2-oxidanylidene-1-phenyl-ethyl]carbamoyl-methyl-amino]methyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-8P3:
2-[(2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]benzoic acid

ChemComp-UJ6:
5-{[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]methyl}-1,3-benzodioxole-4-carboxylic acid

ChemComp-K5Q:
(2S)-6-[(E)-[(2E)-2-hydroxyimino-3H-inden-1-ylidene]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

ChemComp-LOZ:
5-[[(1S,2R)-2-(4-azanylbutanoylamino)-2,3-dihydro-1H-inden-1-yl]methyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-NZL:
5-[[(1S,2S)-2-(6-azanylhexanoylamino)-2,3-dihydro-1H-inden-1-yl]methyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-ONZ:
2-(1,3-benzodioxol-4-ylcarbonylamino)ethanoic acid

ChemComp-U2Z:
[1-[2-(aminomethyl)phenyl]-5-methyl-pyrazol-3-yl]methanol

ChemComp-IMV:
5-[(2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-CWU:
5-[[(1S,2R)-2-oxidanyl-2,3-dihydro-1H-inden-1-yl]methyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-C5Q:
5-(1H-indol-3-ylmethyl)-1,3-benzodioxole-4-carboxylic acid

ChemComp-H75:
2-(4-bromophenyl)-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3(2H)-one

ChemComp-LYS:
LYSINE

ChemComp-Y7N:
5-[(E)-[(2S)-2-(6-azanylhexanoylamino)-2,3-dihydroinden-1-ylidene]methyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-JDX:
2-methoxy-6-[[[2-[(4-methoxyphenyl)methylcarbamoyl]phenyl]methyl-methyl-amino]methyl]benzoic acid

ChemComp-X0P:
2-methoxy-6-[[[3-[(4-methoxyphenyl)methylcarbamoyl]naphthalen-2-yl]methyl-methyl-amino]methyl]benzoic acid

ChemComp-E4F:
5-[[(1R,2S)-2-(5-azanylpentanoylamino)-2,3-dihydro-1H-inden-1-yl]methyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-S3G:
5-[(2S)-4-methyl-2-[(pyridin-4-ylcarbonylamino)methyl]pentyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-4VW:
5-[(2S)-2-[[(4-aminophenyl)carbonylamino]methyl]-4-methyl-pentyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-Q31:
5-[(2S)-2-[[2-(1H-imidazol-4-yl)ethanoylamino]methyl]-4-methyl-pentyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-RVN:
5-[(E)-(2-oxidanylidene-1H-indol-3-ylidene)methyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-H39:
5-[(2S)-4-methyl-2-{[(1H-pyrrol-3-ylacetyl)amino]methyl}pentyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-9PA:
5-[(2S)-2-{[(5-aminopentanoyl)amino]methyl}-4-methylpentyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-4D2:
5-[(2S)-4-methyl-2-[(pyridin-3-ylcarbonylamino)methyl]pentyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-VXO:
5-[(2S)-2-[[2-(1H-indol-3-yl)ethanoylamino]methyl]-4-methyl-pentyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-FYM:
2-methoxy-6-[[[6-[(4-methoxyphenyl)methylcarbamoyl]-1,3-benzodioxol-5-yl]methyl-methyl-amino]methyl]benzoic acid

ChemComp-L0Y:
6-[[[2-(cyclohexylmethylcarbamoyl)phenyl]methyl-methyl-amino]methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

ChemComp-HLR:
1,2-benzoxazol-3-amine

ChemComp-JNS:
5-[(Z)-2-phenylethenyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-IV2:
5-chloranyl-4-methyl-1,3-benzothiazol-2-amine

ChemComp-CBJ:
6-[(5-bromo-2,3-dioxo-2,3-dihydro-1H-indol-1-yl)methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

ChemComp-OM1:
(4-CARBOXY-1,3-BENZODIOXOL-5-YL)METHYL-[[2-[(4-METHOXYPHENYL)METHYLCARBAMOYL]PHENYL]METHYL]AZANIUM

ChemComp-NVU:
2-(1,2-benzoxazol-3-yl)ethanoic acid

ChemComp-K1T:
5-[(2S)-2-{[(4-aminobutanoyl)amino]methyl}-4-methylpentyl]-1,3-benzodioxole-4-carboxylic acid

ChemComp-1TD:
3-[(E)-(2-oxidanylidene-1H-indol-3-ylidene)methyl]benzoic acid

Source
  • human immunodeficiency virus 1
KeywordsTRANSFERASE / STRUCTURE BASED DRUG DESIGN / DNA INTEGRATION / RNA-DIRECTED DNA POLYMERASE / HIV INTEGRASE

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